RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.KK8tAj/RM_25678.ThuDec71841342023 Search Engine = rmblast 2.13.0+ Threads = 32 Dependencies: TRF 4.09, RECON , RepeatScout 1.0.6, RepeatMasker 4.1.4 LTR Structural Analysis: Disabled [use -LTRStruct to enable] Random Number Seed: 1702003292 Database = /dev/shm/rModeler.KK8tAj/GCA_949987585.1_mPipPyg2.1 - Sequences = 243 - Bases = 1895125685 - N50 = 100973200 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 198501199-212679785 | [ 2 ] 184322613-198501198 | [ 1 ] 170144028-184322613 | [ ] 155965442-170144027 | [ ] 141786856-155965441 | [ ] 127608271-141786856 | [ ] 113429685-127608270 | [ ] 99251099-113429684 | [ 3 ] 85072514-99251099 | [ 3 ] 70893928-85072513 | [ 3 ] 56715342-70893927 | [ 1 ] 42536757-56715342 |* [ 6 ] 28358171-42536756 | [ ] 14179585-28358170 | [ 3 ] 1000-14179585 |************************************************** [ 221 ] Storage Throughput = excellent ( 1110.14 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40008011 bp ( 40007011 non ambiguous ) - Num Contigs Represented = 47 - Sequence extraction : 00:02:23 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:20:33 (hh:mm:ss) Elapsed Time Round Time: 00:29:23 (hh:mm:ss) Elapsed Time : 323 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:36 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:35 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 13385 repeats masked totaling 2306261 bp(s). - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10003250 bp Num Contigs Represented = 27 Non ambiguous bp: Initial: 10003050 bp After Masking: 6907420 bp Masked: 30.95 % -- Input Database Coverage: 10003250 bp out of 1895125685 bp ( 0.53 % ) Sampling Time: 00:01:22 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:05:41 (hh:mm:ss) Elapsed Time, 8296 HSPs Collected Number of families returned by RECON: 749 Round Time: 00:07:33 (hh:mm:ss) Elapsed Time : 22 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:48 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:02 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 44172 repeats masked totaling 7404668 bp(s). - TE Masking time 00:00:28 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30004681 bp Num Contigs Represented = 42 Non ambiguous bp: Initial: 30003881 bp After Masking: 20695936 bp Masked: 31.02 % -- Input Database Coverage: 40007931 bp out of 1895125685 bp ( 2.11 % ) Sampling Time: 00:04:21 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283128 Comparison Time: 00:30:43 (hh:mm:ss) Elapsed Time, 24996 HSPs Collected Number of families returned by RECON: 2485 Round Time: 00:36:16 (hh:mm:ss) Elapsed Time : 62 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:05:24 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:00 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 141832 repeats masked totaling 24618418 bp(s). - TE Masking time 00:01:31 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90017228 bp Num Contigs Represented = 70 Non ambiguous bp: Initial: 90015628 bp After Masking: 59947029 bp Masked: 33.40 % -- Input Database Coverage: 130025159 bp out of 1895125685 bp ( 6.86 % ) Sampling Time: 00:13:05 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2548153 Comparison Time: 03:30:57 (hh:mm:ss) Elapsed Time, 94280 HSPs Collected Number of families returned by RECON: 8045 Round Time: 03:48:17 (hh:mm:ss) Elapsed Time : 200 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:15:54 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:15:34 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 456862 repeats masked totaling 79970362 bp(s). - TE Masking time 00:06:24 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270010723 bp Num Contigs Represented = 122 Non ambiguous bp: Initial: 270005106 bp After Masking: 172962092 bp Masked: 35.94 % -- Input Database Coverage: 400035882 bp out of 1895125685 bp ( 21.11 % ) Sampling Time: 00:38:20 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22899528 Comparison Time: 27:15:16 (hh:mm:ss) Elapsed Time, 236126 HSPs Collected Number of families returned by RECON: 33508 Round Time: 28:24:33 (hh:mm:ss) Elapsed Time : 415 families discovered. RepeatScout/RECON discovery complete: 1022 families found Classification Time: 00:42:43 (hh:mm:ss) Elapsed Time Program Time: 34:08:45 (hh:mm:ss) Elapsed Time